The Dark Expanse
by Cybernetic Pony
Summary: Twilight Sparkle and Rainbow Dash find themselves badly injured and separated from their friends, with no memory of what happened. Meanwhile, a mysterious force begins to come to power within the Equestrian mainland. What does this mean for the ponies of Equestria? This is my first story, so feedback is greatly appreciated.
1. Chapter 1

Twilight groaned as she awoke. Above her, light streamed in from a large hole in the ceiling of the cavernous expanse she now found herself in.

"I must have fallen in..." Twilight mused aloud.

Beside her, Twilight heard a soft sound, like a whimper. She turned her head to find Rainbow Dash lying upside down against the wall. Her eyes were clenched shut, and Twilight judged she was in serious pain.

"Are you alright, Rainbow Dash?" She asked, not hiding her concern.

The cyan pegasus weakly opened one eye and looked at Twilight, then attempted to nod. In the act of doing so, however, she tilted her body mass and was rewarded by a resounding flop into the rocky floor of the cavern. Twilight was by her side in the same second.

"Are you ok? Are you hurt?" Twilight asked as she lifted the mare's face off of the ground.

Rainbow Dash looked at Twilight with an expression of utter defeat. She opened her mouth and pointed to it.

"You can't talk?" Twilight asked, guessing at Rainbow's intended meaning.

Rainbow nodded, then pointed to her right wing. Twilight hadn't noticed, but it was stained a bright crimson and bent at an awkward angle. There were also some white structures penetrating it at various points. Twilight gingerly touched it with her hoof, causing Rainbow to jerk away.

"That needs to be taken care of right now," Twilight said as she attempted to use a basic healing spell.

But instead of casting a spell, Twilight felt an intense pain in her forehead. She staggered backwards and placed a hoof on her forehead. It was hot to the touch, like embers from an open fire. She quickly stopped her spell and brought her hoof to her horn. It hurt to the touch, sending a sharp pain all the way down her spine.

"My horn's swollen," she said quietly, "Probably broken from the fall. I can't use any magic."

Rainbow nodded grimly, then grimaced as another pulse of pain shot through her wing. Twilight quickly searched the immediate area, and picked up a branch and a small section of vine that had fallen in with them. She then placed the branch parallel to Rainbow's broken wing, did her best to realign the bone (causing the bruised pegasus to bite her lip in pain), and tied the branch and wing together using the vine segment.

"Is that better?" Twilight asked eagerly.

Rainbow slowly nodded, then gave her wing a few short, slow flaps. The makeshift cast held, and Rainbow gave a weak smile, which was quickly replied by Twilight. She then looked around the cavern with an inquisitive expression on her face.

"We need to find out where we are," Twilight said as she looked up at the hole, "And how to get out of here."

Rainbow nodded and started walking. Twilight quickly joined her.

• • •

"'If you're tryin' ta find me,'" Applejack read with an irritated voice, "Ah've gone ta Canterlot for official royal duties. Ah will be back before 3:00 PM on Tuesday. ~Twilight Sparkle.' Well, it's 4:30 on Wednesday and she still ain't here. Where in tarnation do ya reckon she is?"

"Oh, dear," Fluttershy responded timidly, beginning to pace, "What if she's in danger? Or trapped and scared and hungry with no way to get out? Oh, poor Twilight!"

"Fluttershy, dear," Rarity said, putting a hoof on the yellow pegasus's shoulder to calm her down, "I'm quite sure she can take care of herself. She's probably still at Canterlot. Something probably came up that required her attention. Royal duties can be quite cumbersome."

"And I s'pose you'd know about royal duties," Applejack said in a deadpan voice, earning an annoyed look from Rarity.

"I never claimed to, Applejack," she replied matter-of-factly, "But it's not a preposterous idea. Certainly more likely than Twilight avoiding-"

Rarity was interrupted by the sudden appearance of Pinkie Pie, whose face was an expression of pure worry.

"I just went over to Dashie's house to ask her if she wanted to come to the pond with me, so I went over to her house and used my flying bike, because everypony knows an earth pony can't walk on a cloud like a pegasus can, so I used my flying bike to get to her house, and I went to her door and knocked, and knocked, and knocked again, but she never answered! So do any of you know where Dashie is so I can ask her-"

Applejack put her hoof in Pinkie's mouth to silence her.

"Whoah there, Nelly," she said as she removed her hoof from the other mare's mouth, "Start over again, and this time talk a bit slower."

"Rainbow Dash is gone!" Pinkie cried dramatically, regaining her composure a moment later, "Have any of you seen her?"

"So Twilight and Rainbow Dash go missin' at the same time," Applejack mused, "Somehow Ah don't think that's a coincidence."

"I agree," replied Rarity, "But why would Rainbow Dash go to Canterlot?"

"Ah wonder what those two're doin'," Applejack said, essentially ignoring Rarity, "And why didn't they tell us?"

"Where's Twilight?" Pinkie asked, suddenly noticing the absence of the new princess.

Applejack and Rarity both rolled their eyes.

• • •

The cavern became increasingly dark as Twilight and Rainbow continued walking, but Twilight still noticed that Rainbow was walking with an uneven gait. It appeared she was limping, and it became more noticeable with every step she took. Twilight was about to ask her about it when the rainbow-maned pegasus suddenly fell forward.

"Are you ok Rainbow," Twilight asked, growing more concerned every minute they are stuck in the cavern, "What happened?"

Rainbow attempted to stand back up, but her left foreleg buckled as soon as she put weight on it. Twilight quickly examined it.

"It's broken," she said, her voice lined with incredulity, "What did you do to injure yourself so badly?"

Rainbow wouldn't look her in the eyes, so Twilight let her question go unanswered as she hoisted the crippled pegasus onto her back.

Progress was slower, now. Much slower. Twilight could only walk a fraction of her previous pace, and had to stop frequently to rest (she hadn't carried this much weight without magic since she attempted to restock the library in Canterlot as a filly, and even then she couldn't handle it well. She wasn't allowed in the library for a week after that).

Twilight couldn't help but notice the irony of their situation. Here were two mares, both of whom could fly, trapped in a cavern from which they needed only to fly to escape. As she thought about this, though, realization came to her that her wings weren't broken. But it didn't matter now. Not only were they too far from the hole now to try and relocate it, but Twilight could only barely fly alone, much less while carrying another mare. And there was no way she would leave Rainbow here alone.

Rainbow's head rubbed against Twilight's mane. She had fallen asleep. _Good_, thought Twilight, _She needed that._ She then gingerly lay Rainbow down next to the wall, and lay down herself. She thought then of another irony. Here was Rainbow Dash, a symbol of independence, loyalty, and strength; here was a mare who could not fly, walk, or even speak. She was completely dependent.

_...On me_, Twilight added in her thoughts, _She is completely dependent on me._

This thought struck Twilight like a brick. Responsibility had always been expected of her as Celestia's student, Spike's caretaker, and recently as a princess of Equestria. But never had anypony been so absolutely dependent on her as Rainbow Dash was right now, except maybe Spike in his infant years. Here one of Twilight's best friends, the holder of the Element of Loyalty and a symbol of strength and independence, could not even walk. It was a sad thought, and one that made Twilight even more protective of the cyan mare. As she lay down beside her, a thought formed in her mind. One that stayed with her as she drifted into sleep.

_I won't let anything happen to you._


	2. Chapter 2

Author's note: Thank you for the feedback on the first chapter! This one is a bit shorter. Hereafter, chapters will probably be updated much less frequently (my current aim is one chapter per week, but we'll see how that works), but they will also be much longer.

* * *

><p>Rainbow Dash awoke with a start. She sighed as she remembered the events of the previous day, giving her wing a few slow, painful flaps. She then looked at Twilight, and shuddered. Twilight's memory had been taken from her, but Rainbow could still remember. Not like a normal memory, but in parts, like the memory of a dream. The dream from which she had just awakened was one such memory. She placed her hoof gently on Twilight's forehead, then jerked it back to avoid being burned.<p>

_It's getting worse…_ she thought as she lay back down, still looking at Twilight. _And I can't warn her._

Twilight had assumed her horn was broken, and that was the source of the heat and swelling. But Rainbow knew better. She couldn't recall how, but she knew Twilight's life was in danger, and that her magic would be the catalyst.

_And I can't even warn her_…

A sudden surge of pain shot through Rainbow's wing, and her sudden movement awakened Twilight. She looked at Rainbow with a look of concern, then sighed when she realized what had happened.

"We need to get you out of here," she said, "And into a hospital."

Rainbow nodded, then made the motion of walking with her front hooves. Twilight nodded and carefully placed Rainbow back onto her back, then continued walking down the tunnel.

_She's in danger_, Rainbow thought, _And I can't even warn her_.

• • •

Fluttershy ducked timidly as she opened the door to the library. After a few moments passed without her being greeted, she slowly stepped inside. It was dark, and books and papers were strewn across the floor.

"H-Hello?" She asked timidly, her voice trembling a bit, "Is… is anypony home? Twilight? Spike?"

There was no reply, so Fluttershy gently closed the door and lit a candle.

_I shouldn't be here_, Fluttershy thought as she walked toward the staircase to Twilight's bedroom, _But something's wrong…_ _Twilight wouldn't just-_

"Hiya, Fluttershy!"

Fluttershy screamed, dropped her candle, and hid underneath a nearby desk. But she still found herself face-to-face with the over-enthusiastic pink mare.

"Whatcha doin'?" she asked, seemingly unaware of the heart attack she nearly gave her friend.

"Oh.. hi Pinkie," Fluttershy responded as she regained her composure, "I'm... looking for Twilight."

"Isn't she in Canterlot?" Pinkie asked, tilting her head to the side.

"I don't think so," Fluttershy responded sheepishly, "Something isn't right…"

"It looks like someone threw a party in here!" Pinkie exclaimed, her attention drawn to the messy state of the library.

"Yeah…" Fluttershy replied as she crawled out from under the desk, "But I don't think Twilight threw a party…"

"Hm…" Pinkie thought aloud. She then procured a magnifying glass and deerstalker from somewhere and began investigating Pinkie style.

"Interesting…" Pinkie said as she held the magnifying glass to a note written by Twilight.

"What is-"

Fluttershy was interrupted by a knock on Twilight's door. Fluttershy and Pinkie exchanged confused glances, then Pinkie opened the door. A squadron of royal guards quickly captured both her and Fluttershy.

"You are both under arrest for the kidnapping of Princess Twilight Sparkle."

• • •

Zecora felt a growing sense of unease as she gathered the herbs she needed for her favorite tea. She made this trip nearly every day, and never had she felt so uncomfortable about it.

_Something is in the air tonight_, she thought, _What could it be, that gives me this fright__?_

She heard a rustling in the leaves behind her, and eyed the location warily. After a few moments, she slowly and cautiously walked away from it and gathered the herbs she needed and turned back toward her hut.

_Today is no day to be having fun_, she thought, _Today is a day on which I should run_.

She ran back to her hut, closed the door securely, and placed the herbs on a small table beside her cauldron. She quickly pulled blinds over her windows, then began mixing the herbs with the other ingredients she had.

"Whatcha doin'"

Zecora jumped, then looked down at the filly before her.

"Why, Scootaloo!" she said with a surprised tone, "I have been visited by many, but never by you. Tell me, young filly, why are you here on such a day as this, that makes even me fear?"

"Well," Scootaloo said, looking at the ground, "Somepony told me that Rainbow Dash came into the Everfree Forest, so I came to find her. Do you know where she is?"

"My answer to your question is no," Zecora responded as she returned to making her tea, "And neither you nor me outside must go."

"But-"

"Do as I tell you, and be good," Zecora said, cutting of Scootaloo's protest, "Or you may become the forest's food."

"Fine..." Scootaloo responded in a defeated tone as she sat down and watched Zecora.

• • •

Rainbow sighed. She couldn't stand the idea of being so helpless. She also couldn't stand being carried by Twilight. She was appreciative, of course, but she couldn't stand moving so slowly.

Ahead, the cavern was illuminated by a dim green glow. The source of the glow was a glowing green mushroom that grew in patches along the floor and walls of the cavern. Rainbow knew she had seen them before, but she couldn't recall where. Twilight slowed as she approached them, and carefully examined one.

"We're near the Everfree Forest," she said as she ran a hoof over the smooth fungal surface, "These grew around Zecora's as well."

Rainbow nodded as Twilight began walking down the cavern again. She couldn't help but notice a growing anxiety. Twilight sensed it.

"Are you ok, Rainbow?" she asked as she stopped and looked back to her.

Rainbow nodded. Twilight looked at her for a few moments with an unreadable expression, then turned and continued walking through the cavern.

Rainbow began thinking about her memories. It seemed she could remember more a few moments ago. All she could remember was that Twilight must not fly or use magic, or she would be in serious danger.

_I wish you could hear me_, Rainbow thought, _I wish you knew how much danger you were in…_

But she couldn't remember what danger Twilight was in.

• • •

"Do you understand why you are here?"

Derpy did not respond. She was cold, and the echo of dripping water penetrated through the air.

"I said," the stallion repeated, his tone more commanding, "Do you know why you are here?"

There was a flow of cool air. It was under pressure, and she could feel it more on her neck than on her leg. It was probably from a hole in a pipe. The echoes of the dripping water were also metallic in nature, so she judged they must be dripping onto a metallic surface. She must be in a factory of some kind, but why were there no machines running?

"Yes," she said quietly.

The stallion didn't say anything, but pulled a lever. Derpy felt the chair she was in lay backward.

"Then you know what happens next?" the stallion asked.

"I won't talk," Derpy responded, "I will never talk."

"Suit yourself," the stallion said, "But I can assure you, we will change your mind."

Derpy heard the airlock of a nearby door moments before the cover of the capsule she was in sealed. The last thing she could remember was how cold it suddenly became.

_I will never talk_, she repeated in her thoughts before she fell unconscious.

* * *

><p>Author's Note: What do you think of my organization (i.e. multiple sections of storyline per chapter)? Should I continue doing that, or should I start devoting each chapter to a single storyline element?<p> 


	3. Chapter 3

Author's Note: I updated the last chapter five minutes after it was uploaded, but the changes didn't take place. So there's new stuff there. Enjoy! :)

* * *

><p>Rainbow gazed in wonder at the sight before her. The narrow tunnel opened into a large open space, illuminated by a much larger variant of the glowing fungus they had encountered earlier. A large population of fireflies also inhabited the area, filling the dim cavern with the illusion of stars.<p>

Twilight was also staring at the strange sight, but her expression was more of concern than interest.

"This can't be..." She said softly, closely examining every detail, "...can it?"

Twilight looked around carefully, taking in every detail. Her expression became more concerned with every moment.

"We can't stay here," she said after a moment, a sense of urgency in her voice, "We have to keep moving."

Twilight then continued walking forward. The cave's floor was covered with water, reflecting the fireflies above. Twilight stopped, bent down to it, and dipped her hoof into it. After submerging the entirety of her hoof, she stood back up.

"No way to tell how deep it is," she said to herself, "Better be careful."

Very carefully, Twilight stepped onto a section of the floor that wasn't submerged. It was slick, but she still managed to secure a foothold, and moved forward. She repeated this process with every stone.

Rainbow quickly grew bored of watching Twilight's hoofwork. So she watched the water, admiring the beauty of the image. She didn't know how long they had been down here, but she already missed seeing the sky.

_And flying in it_, she added with a note of resentment.

Rainbow heard a quiet splashing sound behind them, and saw the water begin to ripple from the corner of her eye. She turned her head to watch for further movement, but saw none.

_I must have imagined it.._. she thought, not believing herself.

Rainbow jumped as she heard a much louder splash near them, drawing Twilight's attention from her careful maneuvering. She gasped as her hoof slipped on the stone floor, and she and Rainbow both fell into the water with a splash. A burning pain welled in Twilight's forehead as she fell in, and her vision faded to white.

_I have to find Rainbow_, was her last thought before she lost consciousness.

* * *

><p>Princess Celestia was greeted by fanfare as she entered the Royal Court. Her fellow princesses, Cadance and Luna, were already seated behind a desk, and the defendants stood in chains before them. Celestia sat between Luna and Cadance, an unreadable but certainly not happy expression on her face as she looked at the defendants.<p>

"This Royal Court of Canterlot will now come to order," Luna announced using her Canterlot voice, "The defendants, Fluttershy and Pinkie Pie of Ponyville, are tried with the kidnap and possible attempted murder of Princess Twilight Sparkle."

"Please give us your account, Captain Sentry," Celestia said to an orange royal guard, "Why do you suspect Fluttershy and Pinkie Pie?"

"They were found, and captured, in the library shortly after the Princess's disappearance, your highness."

"Can you explain why you were in the library?" Celestia asked as she turned her attention to Fluttershy and Pinkie.

"W-well," Fluttershy said, her voice shaking as much as she was, "Applejack found a note that said Twilight was in Canterlot, and was late. But..."

"But..?" Celestia asked after a moment.

"I... I'm not sure. Something didn't seem right. So I went to see if I could find anything strange."

"Did you?" Celestia asked, "Was there anything out of the ordinary?"

Fluttershy opened her mouth, but was cut off by Pinkie, who was again wearing a deerstalker and holding a bubble-blowing pipe in her hoof.

"If I may draw your attention to Exhibit A," she said with a mock English accent as she gave the princesses the note Applejack found, "You may recognize the note found by Applejack at the scene of the crime. Now, compare that to exhibit B, a letter written by Twilight."

"These aren't written by the same pony," Cadance said as she held the two letters side-by-side, "So you're suggesting that the Canterlot notice is a fraud?"

"Precisely," Pinkie said, "But that isn't all."

She quickly set up a projector and screen, then showed a picture of Twilight's library as it was when she and Fluttershy were investigating it. Fluttershy didn't notice a camera earlier.

But then again, she thought, Pinkie is Pinkie.

"This picture shows two important things," Pinkie continued, "What do you notice?"

"Obviously the mess," Luna said in a confused tone, "But what else?"

"Where's Spike?" Pinkie asked as an answer, "Twilight would have left him to take care of Owlowiscious if she were going on an extended trip. And on that note, where is Owlowiscious? Not in the library."

"Thank you for your convincing argument, Pinkie," Celestia said with a smile.

Pinkie returned to Fluttershy's side, now also wearing a fake mustache for no apparent reason.

"How did you do all that with these chains on?" Fluttershy asked in a highly confused tone.

"Chains? Oh yeah!" She said as she started laughing, "I forgot I had these on!"

Fluttershy could only stare at her in confusion.

* * *

><p>Scootaloo sighed as she blew the hair out of her face as she lay on her back. Staying put and out of trouble was hard. She wanted to go find Rainbow Dash. And she had half made up her mind to sneak out and do so when she heard a hissing noise from outside.<p>

Zecora heard it too, and was now looking at the door with a concerned look on her face. Slowly and quietly, she moved to Scootaloo and leaned toward her.

"Quickly, find the handle on the floor," she whispered urgently, "Pull it, and go through the door."

Zecora pointed to an adjacent room and nodded to Scootaloo, then walked into another room. Scootaloo went into the room Zecora motioned to and searched the ground for a handle. After a few moments of searching, she found and pulled it. It opened a hatch-style door, which she quickly jumped through. A moment later, she was joined by Zecora, who was carrying a rack of potion samples.

"What're those?" Scootaloo asked, "What do they do?"

"Hopefully you will not have to see," Zecora said as she closed the hatch door above her, "Because as soon as you do, you will have to flee."

Scootaloo was silent for a moment as she stared thoughtfully at the floor. Zecora it her hoof on the filly's head for a moment, then walked to the end of the room, out of which opened a fairly large rock tunnel. She rolled a large wooden plate over it, and proceeded to bar it.

"What made that sound?" Scootaloo asked, suddenly expressing fear, "And why?"

"Some dark story is unfolding, I fear," Zecora said as she placed her hoof on Scootaloo's head, "But, for now, we are safe here."

Scootaloo was still concerned, but she felt comforted. She let out a small yawn and smiled.

"You need your rest," Zecora said as she pulled some blankets out of a closet and gave them to Scootaloo, "Do not fear; everything will be for the best."

Scootaloo made a pallet in the floor from the blankets and quickly fell asleep. Zecora lay down next to her, her eyes locked on the hatch door.

* * *

><p>Twilight slowly opened her eyes. Her forehead was burning, and her legs were bound to the table on which she lay. She struggles against the restraints for a few moments, then examined her surroundings. She was in a room carved from rock, and the doorway was covered in ornate symbols and decorations. The door was wooden, and painted a dark blue with a symbol of a moon in it's center.<p>

A cloaked figure walked beside her, dipped it's hoof into a small bowl of water, and placed the hoof onto Twilight's forehead. The pain was insatiable, and she could hear a sizzling sound at the contact.

"You are under a dark spell," the cloaked mare said as she repeated her previous action, "I have never seen so strong a magic."

Twilight only barely heard what she said. She was doing everything she could to keep from screaming in pain.

"It hurts, does it not?" The elderly mare asked as she repeated her procedure a third time, "But how badly?"

"It..." Twilight began, struggling to find the words, "feels like hot coals pressed- Ah!"

"I see," the mare said as she applied pressure to Twilight's forehead, "And this makes it hurt?"

The only sound Twilight could muster was a slight whimper, so the mare removed her hoof from the alicorn's forehead.

"This is the work of a powerful dark magic," she said as she put the bowl away, "There is little I can do to counter it. Do you have any memory of it?"

Twilight shook her head. Then her eyes widened.

"Where is Rainbow Dash?!" she asked urgently.

"You will learn soon enough," the mare replied, "Right now the focus is you. Good night."

The mare left the room, leaving Twilight tied to the tabletop.

_I will never let anything happen to you.._

* * *

><p>"Sir, we have no reports of unusual activity," the stallion said with a salute, "Everything seems stable."<p>

"Good," replied the grey stallion as he ascended a few steps, "Prepare the machine."

"Yes sir," the younger stallion replied as he left.

_Soon, _the grey stallion thought, _Everything will fall into place. _


	4. Chapter 4

Twilight closed her eyes and took a deep breath, relaxing her muscles. She had accepted the fact that she couldn't escape from her present situation, and a part of her didn't want to. Although being bound to a table wasn't the most comfortable of predicaments, it did offer a sense of security.

_As paradoxical as it seems,_ Twilight noted.

Twilight turned her head to face the door, and examined the figures carved into the doorframe. She decided it was some ancient form of writing, but she couldn't quite place it. However, she found that she could read some of it. It seemed to be in praise of the moon and stars.

_I thought so_, Twilight thought as she looked at the rock ceiling.

Twilight had read about this place, but she didn't think it actually existed. She thought it to be nothing more than an ancient legend. And yet here she was, experiencing it in reality.

The old mare came into the room, carrying a large bag. She set the bag down next to the table Twilight was on, then looked her in the eye.

"Who are you?" She asked with a tone of hostility, "Where do you come from?"

"My name is Twilight Sparkle," Twilight replied, "And I come from Ponyville."

The mare gave a sigh of relief and reached into her bag. She pulled out a cloth, soaked it in a purple liquid, and wrapped it around Twilight's horn. The burning pain instantly subsided, and the swelling lessened. But it also felt like something was missing.

"It is as I thought," the mare said as she placed a hoof on Twilight's forehead, "This will help with the pain and swelling, but it will also prevent your use of magic. You are under the effects of a dark magic. If you use magic, you will be killing yourself."

Twilight stared at her in disbelief.

"You mean I can't use my magic anymore?" Twilight asked incredulously, "Is it permanent?"

"I do not know," the mare replied as she pulled some kind of cloth band out of her bag, "That is dependent on the nature of the magic, the intent of the caster, and your own decisions. Stay still."

The mare unbound Twilight's hooves, then tied them together with the band and set her on her feet. They offered little movement, but she could walk, at least.

"Do you know where you are?" The mare asked as she tied the opening of the bag.

"Yes," Twilight said hesitantly, "But I don't know why, or how."

"You likely do not know the full story either," the mare said as she walked to Twilight, "Sit down, and I will tell you our story."

* * *

><p>Tears streamed from Luna's face as she flew through the cold air. She stopped when she came to the edge of the Everfree Forest, then sat behind a boulder.<p>

"She just doesn't understand," Luna said quietly, "She just... Just..."

She let out a cry of rage, then picked up a large log with her magic and flung it toward the castle. It fell far short from the castle, but it still calmed Luna somewhat.

Luna's ear twitched as she heard the crying of a small filly. She looked down and there, next to where the log had been, was a crying yellow unicorn filly. Luna looked around, then picked the filly up.

"It's ok," she said, "I understand you. We have both been abandoned..."

She then had an idea. Celestia had her empire, so why couldn't she? She would gather together everypony unhappy with the current regime, and create her own.

"You're going to be ok," Luna said to the young filly, "It's all going to be ok now."

_Yes_, she thought as a devilish smile spread on her face,_ It's perfect! Just perfect!_

She hugged the filly, then flew to the nearest town to begin the New Lunar Republic.

* * *

><p>Luna stood on the peak of Mount Canter, looking down at the Everfree Forest. Beside her stood Moondancer, her most trusted advisor, and the mare she found abandoned as a filly in the Everfree Forest. Behind them stood an army of a thousand strong, each wearing dark armor and armed with spears.<p>

"May the moon live forever," Moondancer said as she looked at the celestial sphere, "For ever and ever."

Luna nodded slowly, then looked back to her army.

"This is the moment you have all trained for," she said with a commanding tone, "Let not that effort be in vain! The time has come! Move!"

Luna and Moondancer took to the sky as her army advanced toward the forest. As they marched, they began to chant:

_ For Luna!_

_ For the moon!_

_ For the Lunar Republic!_

As they neared the castle, Celestia met them with her royal guards.

"Luna!" She cried, "What are you doing!?"

"I am going to overthrow your tyrant rule, sister!" Luna hissed as se raised her hoof into the sky, "Charge!"

Her army rushed forward to meet Celestia's, and thus began the Battle of the Eclipse. They fought for hours before Celestia's army prevailed. But Luna and Celestia were now in the castle.

"The moon will prevail," Luna yelled maniacally as her form began to change, "I will not allow my night to be forgotten!"

"Please, sister!" Celestia pleaded, "Please come to your senses!"

Luna answered Celestia with a well-timed blast of magic. The impact knocked her into the castle's lower level, near where the Elements of Harmony were located.

"I'm sorry, sister..." Celestia said as she entered the room in which the elements were kept.

* * *

><p>Moondancer breathed heavily as she was surrounded by royal soldiers. Tired and outnumbered, she dropped her weapon.<p>

"I am sorry, Luna," she said as she was bound, "My princess."

A loud scream penetrated the air, and Moondancer looked up to see Luna surrounded in rainbow streamks and screaming in pain. A moment later, she was gone, and her image took it's place on the moon. She fell to her knees as tears came to her eyes.

"No!" She cried as Celestia approached her, "You monster! You have no idea what you've done!"

Celestia placed her hoof on Moondancer's shoulder as a tear fell down her face.

"You've killed her!" Moondancer continued accusing as she bit at Celestia's hoof, "You killed my princess! My mother!

Celestia pulled her hoof back, looked at Moondancer for a moment longer, then sighed and turned toward the castle.

"Take her away," Celestia said quietly, her voice weak and inconsistent.

_You killed my mother..._

* * *

><p>"Moondancer," the mare continued, "Has become a name of custom for my family. It was my grandmother's name, my mother's name, and mine."<p>

That's what I was afraid of... Twilight thought.

"I... I'm sorry to hear that," she said quietly as she looked at the ground.

"Now we wait," Moondancer continued, "For the coming of our Princess of the Night."

Twilight blinked. She wasn't welcome here. If they knew she was Celestia's student... Twilight couldn't bear to think about it, but she knew she had to leave as soon as possible.

"Where is Rainbow Dash?" She asked, looking Moondancer in the eye, "May I see her now?"

Moondancer started to say something, then stopped and nodded.

"Follow me," she said as she opened the door and stepped out, "Right this way."

* * *

><p>Rainbow's hoof and wing were properly bandaged, and se was sleeping peacefully. Twilight was relieved that she could finally get some rest. Lately she had been met with one misfortune after another.<p>

Twilight walked outside and looked around. The village was carved into the sides of the large room, with walkways running the perimeter at various heights, linked together with rope ladders. There were no lights outside of the glow of the fungi and the flashing fireflies. It really was a beautiful sight.

"What do you think?" Moondancer asked as she stood beside Twilight.

"It's beautiful," Twilight replied, "And so elegantly designed."

Moondancer nodded as she looked at the movement of ponies on the other side of the large expanse.

"Indeed," she said quietly, "How long do you plan to stay?"

"I'm not sure," Twilight replied, "but at least not until Rainbow heals."

Moondancer nodded again, then walked away. Twilight watched her for a moment, yawned, then walked back into Rainbow's room, sat on a couch, and fell asleep.

* * *

><p>Celestia walked with Fluttershy and Pinkie as they left the Royal Court. Fluttershy was trembling, but Pinkie seemed completely oblivious to the events that had transpired. Celestia was just glad everything had gone by so smoothly.<p>

"Do you know where Twilight is?" Celestia asked with a hint of concern, "Or where she could have gone?"

"No," Fluttershy responded, her voice shaking as much as she was, "And that's what concerns me..."

"Me as well," Celestia said as she looked at the ground, "Me as well..."

"We could ask Discord," Fluttershy suggested, "Maybe he knows where she is. Or maybe he could find her if he doesn't."

Celestia thought for a moment, then cast a summon spell. Within moments, the chaotic dragon appeared, dressed as a butler.

"You called?" He asked with an English accent.

"Yes," Celestia responded, still not fully trusting the discordant being, "Do you know where Twilight Sparkle is?"

"What, did you lose her?" The draconequus asked with a grin before laughing at his own joke.

Celestia raised an eyebrow.

"Oh, you're being serious," Discord responded with a solemn expression before laughing again, "Let me laugh even harder!"

Celestia cleared her throat.

"Oh, fine," Discord responded with a frown, "You really are no fun at all. You know that. No, I do not know where Twilight is. But I can find her."

Discord snapped his fingers. But instead of juggling a purple princess, he found himself holding a white unicorn.

"Hm. That's odd even by my standards," Discord said as he put the unicorn down. She took a few steps backward away from Discord and looked around, adjusting her shades.

"So, uh..." She said in a confused tone, "Did I miss a gig or something?"

Pinkie donned a jovial and excited expression and began to talk, but Celestia cut her off.

"No, Vinyl," she said, struggling to keep a calm tone, "This was an accident. You may go."

"Ok, cool," Vinyl said as she walked toward the door, "Have a good day, and stuff."

Celestia watched her with a hint of curiosity. The only pony she knew that could be teleported and not be phased by it was Pinkie, and even she would show some surprise. Or maybe she wouldn't. You could never really tell with Pinkie.

Discord snapped his fingers again, this time summoning an orange pegasus. She was holding a milkshake, and was in the act of sipping it. She stopped and looked around suspiciously, straw still in mouth, until she saw Princess Celestia. She immediately stood to attention, causing the milkshake to drop to the floor. Pinkie stared at it with a shocked and sad expression.

"Yes, your highness?" She asked in an authorative tone, "You called?"

"It was a mistake," Celestia said, glaring at Discord, "You are free to go, Spitfire."

Spitfire looked at her milkshake, then at Celestia, then at Discord, then at Celestia again. Celestia gave her a few bits, then she walked toward the door. Celestia glared at Discord as he began to do it again.

"Are you trying to be funny?" She asked with a highly aggravated tone, "Because you're not."

"Actually," Discord replied with an equally annoyed tone, but his not directed at anyone in particular, "I'm not. Something is preventing me from finding Twilight, and causing my magic to be deflected."

Celestia's look of annoyance was replaced with one of concern. Discord summoned a chair and a glass of chocolate milk, and sat down to think. Celestia noted with surprise that he actually drank the milk, and not the glass.

"This has never happened to me," Discord said with an annoyed and slightly confused tone, "And I don't like it at all. This means something out there has magic equally powerful as mine, if not more so."

Celestia blinked. If Discord could send the whole of Equestria into a state of chaos with the snap of his fingers, what was this new force capable of doing?

_And it has Twilight_, she added, her anxiety now higher than ever.

"What about Spike?" Fluttershy asked timidly, "Maybe he knows something. Can you summon him, Discord?"

Discord snapped his fingers, and the young dragon appeared. He was tied up, and blindfolded. Fluttershy gasped and immediately set to untying him.

"Are you alright?" She asked as she removed his blindfold, "Are you ok, Spike?"

"Y-yeah, I think so," he replied with a dazed expression and detached voice, "Where am I?"

"You're in Canterlot," Fluttershy said quickly, "What happened? Do you know where Twilight is?"

"Twilight?" Spike asked, his eyes widening, "Twilight! She was kidnapped!"

"By who?" Celestia asked with a growing concern, "Who kidnapped her?"

"It was..." Spike said as he struggled to remember, "Um... I can't remember. All I remember is blue."

"The color?" Celestia asked.

"Yes," Spike replied, "I remember blue and purple... That's it."

Celestia looked down, trying to piece the information together. The purple was likely Twilight, so it was likely something blue that took her. And it had to be something powerful to take Spike's memory and deflect Discord's. So maybe a blue unicorn?

"Dashie is also gone," Pinkie added, her voice now growing concerned, "I bet the blue was her! She and Twilight were kidnapped together!"

Celestia looked at Pinkie, trying to piece together a valid argument.

_An alicorn princess and a Wonderbolt-in-training..._ She thought, _That's an odd grocery list for a villain. What could anyone need with them?_

"We still don't have enough information," Celestia said with dissatisfaction, "But we do have a start. We need to find more answers. Fluttershy, Pinkie, please continue your investigation of Twilight's library. Bring Spike with you. Discord, try to locate the source of the deflection, if you can. I will try to find any connections that I can."

Everyone nodded except Discord, who was reading a book. He held up a finger, read for a few minutes longer, then snapped his fingers. The book, the chair, and the spilled milkshake all disappeared. He then appeared in military garb, gave Celestia a salute, and disappeared. Pinkie put Spike on her back, then the two walked toward the door. Celestia watched them, a strong sense of unease beginning to take hold.

_I have to find Twilight..._ She thought as she walked toward the courtroom.

* * *

><p>Scootaloo stretched as she awoke, then began to look around. She was still in Zecora's cellar. Zecora was lying behind her, asleep. It was dark, and quiet, and scary. Scootaloo felt herself begin to shake.<p>

"Zecora?" She asked, giving the zebra a nudge to wake her up, "Zecora, are you awake?"

Zecora opened one eye and looked at Scootaloo, then quickly examined her surroundings. She then looked back to Scootaloo and studied her face for a moment.

"You are afraid?" She asked calmly and quietly.

Scootaloo nodded, a small frown on her face.

"I also was, at your age," the zebra said with a warm smile, "And still am, today. But if I look my fear in the eye, and tell it to leave me be, it goes away."

"Y-you mean, all I have to do is tell it to go away?" Scootaloo asked, a confused look on her face, "And it will?"

Zecora nodded and rubbed Scootaloo's head. She then uncovered the tunnel she had covered the previous night.

"This leads outside of the Everfree," she said with a nod to the entrance, "It is not safe here; we must leave."

Scootaloo nodded and followed Zecora into the dark tunnel.

* * *

><p>Rainbow slowly opened her eyes and looked around. She was in a room carved from rock, and her leg and wing were both bandaged. The pain was still present, but no longer as unbearable.<p>

_Where am I?_ she thought as she sat up and examined the room.

Aside from the bed she was in, there was a table, a couch, and a door. On the couch, Twilight lay sleeping.

_She must be exhausted,_ Rainbow thought. Everything she's been through...

Rainbow lay back down, thinking about everything that happened since they got down here. It seemed unnatural, that all this could happen to the two of them in such a short time. The more she thought of it, the stranger it seemed. But her thoughts were interrupted when an elderly mare entered the room.

"Ah," she said when she saw Rainbow, "You are finally awake."

"Who are you?" Rainbow squeaked painfully.

"You have regained control of your voice," the mare said, "That is good. Just don't lose it again."

Rainbow nodded, then gave the mare an expectant look.

"Oh, you wanted to know who I am, yes? Very well. I am Moondancer, descendant of the Daughter of Night. And who might you be?"

"I'm Rainbow Dash," the cyan pegasus said, her voice breaking inconsistently, "Head of the Cloudsdale weather tea-"

She felt a sudden stinging pain in her throat, and instantly brought her hooves to her throat. Moondancer procured a glass of water and squeezed the juices of a root into it. She then gave it to Rainbow.

"Drink this," she said softly, "It will heal your throat."

Rainbow took the strange concoction and drank it, then coughed violently. It was disgusting, and only made her throat hurt worse. But after a moment, she felt the pain begin to subside.

"Thanks," she said, her voice slightly stronger, as she gave the glass back.

"You are welcome, Rainbow Dash. How are your injuries?"

Rainbow moved her hoof and wing slightly. They still hurt, but nowhere near as badly as they did earlier.

"Much better," she said with a smile.

"Good," Moondancer said as she placed the glass into her bag, "Now try to stand."

Rainbow nodded and slowly brought her hooves to the ground. She closed her eyes as she put her full weight on them, then looked down when she didn't fall. Excited, she took a few steps forward. She had to do it with a slight limp, but she could walk.

"Very good," Moondancer said, paying close attention to her speed and pattern of walking, "I would not suggest trying your wing though. It is much more sensitive."

Rainbow nodded, then looked at Twilight.

"Who is she?" Moondancer asked, "I can tell she has an important role in Equestria."

"She is Celestia's most trusted assistant," Rainbow said with a nod, "And fellow princess of Equestria."

"I see," Moondancer said with a look of distast on her face, "So she and Celestia are the only princesses of Equestria?"

"What? No," Rainbow replied, giving Moondancer an odd look, "They're just two of them. There are four. Celestia, Twilight, Cadance, and Luna."

"Luna?" Moondancer said with an excited voice, "Luna is free?!"

"Well, yeah," Rainbow responded, "She rules alongside her sister. After Twilight defeated her nightmare form."

"Did she now?" Moondancer said, a look of rage becoming apparent on her face, "Thank you for your cooperation, Rainbow Dash."

"Huh?" Rainbow asked with a tilt of her head, "Cooperation?"

"Nevermind," Moondancer said as she glared at Twilight, "Make yourself comfortable, but don't leave this room."

"Ok?" Rainbow said as Moondancer left the room, "That was... Yeah."

_Now what was it I was going to warn Twilight about?_

* * *

><p>Derpy glared at the grey stallion as he secured her hooves onto the arms of the chair.<p>

"You'll never get away with this," she said, her voice lined with anger.

"I wouldn't have to if you would cooperate," the stallion responded, "But it is a shame. There's a certain beauty in your resistance."

He looked Derpy in the eye for a moment, then turned and walked to the control panel.

"Start it," he said to the younger stallion.

The younger stallion pressed a few buttons, then pulled a lever. Bolts of electricity shot around Derpy as the door of the machine closed.

"It won't be long now," the grey stallion said as he watched the machine, "And we'll have all the cards in our hands."

"What about-"

"Don't worry about them," the grey stallion said, cutting the younger one off, "They have been taken care of. Now we only have to worry about the one."

"How can you be so sure?"

"I have my ways. Go check the readings."

The younger stallion nodded, then hurriedly walked out of the room.

The older stallion watched as the door of the machine opened, and Derpy stared ahead blankly.

"Are you willing to talk now?" The stallion asked, raising an eyebrow.

"Yes," Derpy replied.

"Good. Tell me everything."

* * *

><p>Author's note: This is where things start getting fun.<p> 


	5. Chapter 5

Twilight awoke to the sound of drumming in the distance. Lifting her head, she scanned her surroundings and found Rainbow pacing. She noted that the pegasus was walking with a slight limp.

"Rainbow?' Twilight asked as she sat upright, "Is something wrong?"

"I'm not sure," Rainbow said in a raspy voice, "I just..."

Rainbow stopped pacing as she started coughing. As the fit ended, Rainbow stared at the ground for a moment, then cleared her throat and began pacing again.

"You're voice is still weak," Twilight noted as she got to her hooves, "And from the looks of it, so is your leg. Are you sure you should be walking?"

Rainbow stopped pacing and stared at the ground for a moment, then sat down. Twilight nodded, then looked to the window. She hadn't noticed before how small it was.

_Like a cell..._ she thought with a hint of anxiety.

A choral singing now began to rise over the drumming outside. Twilight walked to the window and looked out. The glowing fungus still stood in the center of the cavern, surrounded by the flashing fireflies. She mused for a moment how the fungus was able to achieve such an illustrious glow, but her thoughts quickly returned to the music. She strained her eyes against the dim light, and found ponies standing on the various walkways, all facing the fungus in the center. On top of it, she now noticed, stood Moondancer.

_What in Equestria... _thought Twilight, _What are they doing?_

Moondancer raised a hoof to the cave ceiling, and Twilight saw that her horn was glowing. A figure of the moon was illuminated on the ceiling of the cavern, followed by a loud rumbling. Slowly, with a cloud of dust and crumbling rocks, a circular platform began to lower from the ceiling. As it did so, the fungus split open and began to unfold. It continued unfolding until it had formed a platform that very nearly touched the walkways at the cave's perimeter. The stone platform lowered onto the center of the fungus as ponies lay down wooden slats to cross the gap.

On top of the stone structure was a large black orb radiating a purple fog. Moondancer placed a hoof on its side, an expression of admiration on her face. She then looked over the crowd, an evil grin spreading on her face.

"Today," she said to the assembled group, "We come out of hiding. Today our voice will become heard. Today..."

Moondancer looked back to the orb and rubbed her hoof against it. The fog began to swirl about it, and Moondancer's grin became more menacing.

"Today," she repeated, more quietly, "We unleash our untampered force!"

Twilight scampered away from the window, eyes wide with fear, as Moondancer pounded a hoof against the orb. It shattered like glass, and a growing cloud of fog took its place. It grew quickly, filling the cavern and blocking out the light of the fireflies. The crowd cheered maniacally, their eyes filled with purple, as evil eyes opened within the cloud of fog. The crowd began to sing:

_The Lunar Reign is nigh._

_Let the darkness rise._

_As our night conquers the sky,_

_Witness the last moonrise!_

"Come on," Twilight said, "We have to get out of here. Now."

Twilight tried to open the door, but found she could not. It had been barred shut from the outside. She quickly scanned the room, but could find nothing. She leaned against the wall and sighed.

"Maybe..." she said, her voice sounding desperate, "They don't know who we are. We're still their friends. They don't know I was Celestia's student. Maybe they won't..."

"Actually," Rainbow said, looking down, her voice broken and quiet, "I told them..."

Twilight stared disbelievingly at her for a few moments, then looked at the ground.

"We are at their mercy."

* * *

><p>Shivers went through Scootaloo as she and Zecora walked through the tunnel. It was cold, wet, scary, and dark. She looked carefully at Zecora's face, and sighed when she couldn't find even the slightest trace of fear. Zecora looked at her for a moment, then looked back ahead. The zebra had already established that now was not a time to interrupt her with questions and useless comments. She was clearly deep in thought as they walked, and if her expression was any indication, they were not pleasant ones. So she looked back ahead and pressed on, determined not to be scared.<p>

Only moments after she had made this resolution, however, the ground began to shake violently, and the roof began to crumble. Zecora began running.

"Hurry, my filly!" She cried as she dodged falling rocks, "Be swift on your hooves-Quickly!"

Scootaloo heeded her advice, and began to run, dodging the falling debris. After a few moments, the crumbling stopped.

"What was that?" Scootaloo asked, panting.

"I do not know," Zecora responded, looking closely at the tunnel's roof, "It is not safe here; we must go."

Scootaloo nodded and followed Zecora as she continued walking down the tunnel, faster now than before.

"Where are we going?" Scootaloo asked.

"Away from here," Zecora replied flatly, "There is too much now that causes fear."

"Right..." Scootaloo said, less than satisfied with Zecora's answer.

Zecora gave Scootaloo an odd look, then continued walking. Scootaloo stopped for a moment and looked behind her. Then, with a sigh of defeat, she followed Zecora.

* * *

><p>"Luna," said Celestia, a hint of concern in her voice, "Are you alright?"<p>

"I'm not sure," Luna replied, looking down, "I feel..."

She shook her head, then looked back at the other two.

"It's nothing," she said, "We have Twilight to be concerned about right now."

Celestia and Cadence nodded.

"What is our plan of action?" Cadance asked as she looked out of the window.

"You need to make sure nothing strange is happening at the Crystal Empire," Celestia said, "And that Shining Armor knows about the current situation. As for Luna and I, we will stay here for now. Until we know more about the magic Discord mentioned, we should bring no attention to it."

"I agree," Luna said, "We should not create a panic until we know more about the threat at hand."

Cadance nodded, then flew out of the window.

"We must remain vigilant," Celestia said as she looked out of the window, "Whatever this is, it has Twilight. We must be careful to ensure we are not next."

* * *

><p>"The one day the train stops working," Fluttershy said with an uncharacteristic anger in her voice, "How are we going to get to Ponyville now?"<p>

"Well, duh!" Pinkie said enthusiastically as she pointed at the small town in the distance, "We walk, silly! It's not far. We can get there!"

"Oh..." Fluttershy said, her voice quiet, "It's far enough..."

"What seems to be the problem here?" An orange pegasus asked as she walked up behind them, "Anything I can help with?"

"Hi, Spitfire!" Pinkie said as she bounced joyfully a few times, "We're just about to go to Ponyville-"

"But the train isn't working," Fluttershy interjected, "Oh, sorry Pinkie..."

"Well," Spitfire said as she looked at the small town in the distance, "I can help with that. No problem at all."

Without another word, Spitfire flew off into the distance. Fluttershy and Pinkie watched her until she was out of sight, then exchanged confused glances.

"That didn't help very much," Fluttershy said as she looked at Ponyville, "Maybe we should just start walking..."

"Yep," Pinkie said as she bounced forward, "We'll be there in no time!"

"I don't know if- Ah!"

Fluttershy suddenly found herself lifted off the ground. She screamed as she started moving forward at an alarmingly high speed, then closed her eyes when she realized flailing would do her no good. A few seconds later, she felt ground under her hooves again. Opening her eyes, she found herself in front of Sugarcube Corner. She looked behind herself just in time to see Soarin set Pinkie down.

"I hope this is close enough," Spitfire said beside Fluttershy, "I didn't know exactly where you were going."

"Oh, yes," Fluttershy responded, "This is close enough. Thank you."

"No problem. Need anything else? We don't have to be anywhere until tonight."

"We could use some help investigating Twilight's library," Pinkie said exuberantly, "So we can figure out where she went!"

"Ok," Spitfire said with a shrug, "I can do that. You cool with that, Soarin?"

Soarin nodded, and Pinkie started bouncing joyfully.

"Ok," Fluttershy said, "I'll see if I can find Rarity and Applejack. I'll meet you there."

The other three nodded, so Fluttershy turned toward Carousel Boutique. As she walked down the street, she noticed that there were no ponies outside, and that all the shutters were closed.

_Why is everything so quiet?_

* * *

><p>Twilight awoke with a start and quickly sat up. She quickly surveyed her surroundings and found that she and Rainbow were both lying in wooden frame beds. She put her hoof to her head as a headache began to come.<p>

_What happened?_ she thought, confused, _Where am I, and how did I get here?_

She looked around the room. It was small, and in the corner was a bookshelf with a few small trophies displayed on it. There were also some pictures on the wall. One was a grey unicorn stallion, one was a painting of Starswirl the Bearded, and one was of a white unicorn she had never seen before. She noted with interest a large discolored square on the wall, where it appeared a picture used to be.

Judging from the light coming through the window, Twilight assumed it was morning. So she got out of the bed and walked toward the door. It opened before she got to it, and a familiar blue unicorn stepped through it.

"Good morning, Twilight," she said, "I'm glad you're awake. There's breakfast downstairs if you're hungry."

With that she left and closed the door, leaving a dumbfounded Twilight. She blinked a few times, then stared at the ground.

_Why do I not remember how I got here_? she thought, her mind desperately searching for an answer, _Why can't I remember anything?_

* * *

><p>"I knew I shouldn't have trusted you with this," the grey stallion said as he looked at the screen, "Why did you do it? They were right where I needed them to be."<p>

"There are better ways of handling the situation than just killing them," a green unicorn replied as she levitated a clipboard to the stallion, "Besides, they might prove useful yet."

The stallion took the clipboard and looked over it, then an evil grin spread across his face.

"Yes, point made. Very good, Windlawn. You deserve a raise. Go wait for me in my office."

Windlawn nodded and walked out of the room. Moments later, a dark blue pegasus came in.

"What do you want?" The grey stallion said as he put the clipboard on top of a piece of electronics and looked at the monitor again, "Make it quick, Celsius. I'm busy, and you should be too."

"Is it really necessary?" Celsius said, his voice slightly nervous, "To include Rainbow Dash in this?"

The grey stallion grinned slightly, then turned to face the pegasus.

"Yes, Celsius, it is. You know as well as I do that she poses a threat to this operation, if left unchecked. You can thank Windlawn for sparing her life. Now get to work, we have a lot to do."

Celsius stared at him for a moment, then walked out of the room. The stallion turned back to the screen.

_You're lucky, Twilight Sparkle. Enjoy your freedom while it lasts._

* * *

><p><em>Author's Note: <em>Big thanks to WubWorthyBrony for letting me use his OC Celsius! He will be playing a more integral role in later chapters. On another note, I will be updating this story every weekend or so. Probably around Sunday. Anyway, hope you enjoy it!


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